Section 35 of the CGST Act, 2017 requires assessee to keep & maintain a true and correct account of many thing including ''stock of goods".
Rule 56 of the CGST Rules, 2017 further elborates about these requirements including with regards to various stocks.
So, GSTR-2A got limited role to play. Its your books of accounts and other records which Dept. will primarily check to arrive at their conclusions. And keeping and maintaining those accounts / records is your responsibility.
From your query, I have not understood why are issues faced by you and what is your legal arguments therefor. Can you please elaborate?
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.